ArticleBioinformatics (Oxford, England)2024
MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Reliable Inference of Phylogenomic Relationship via Assembly-Based Strategy Accommodating Raw Reads and Proteins.Molecular ecology resources · 2026Article
- CamK-DB: A k-mer MinHash fingerprint database for reference-free genotyping of Camellia accessions.GigaScience · 2026Article
- MELO-ED: learning locality-sensitive multi-embeddings for edit distance.bioRxiv : the preprint server for biology · 2025Article
- PhyloTune: An efficient method to accelerate phylogenetic updates using a pretrained DNA language model.Nature communications · 2025Article
- Haplotype-resolved and chromosome-level reference genome assembly ofHorticulture research · 2025Article
- PhytoKeys · 2025Article
- Assembly-free reads accurate identification (AFRAID) approach outperforms other methods of DNA barcoding in the walnut family (Juglandaceae).Plant diversity · 2025Article
- Chromosome-level subgenome-aware de novo assembly provides insight intoGenome research · 2024Article
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7 authors.
Funding
Abstract
motivationConstructing a phylogenetic tree requires calculating the evolutionary distance between samples or species via large-scale resequencing data, a process that is both time-consuming and computationally demanding. Striking the right balance between accuracy and efficiency is a significant challenge.
resultsTo address this, we introduce a new algorithm, MIKE (MinHash-based k-mer algorithm). This algorithm is designed for the swift calculation of the Jaccard coefficient directly from raw sequencing reads and enables the construction of phylogenetic trees based on the resultant Jaccard coefficient. Simulation results highlight the superior speed of MIKE compared to existing state-of-the-art methods. We used MIKE to reconstruct a phylogenetic tree, incorporating 238 yeast, 303 Zea, 141 Ficus, 67 Oryza, and 43 Saccharum spontaneum samples. MIKE demonstrated accurate performance across varying evolutionary scales, reproductive modes, and ploidy levels, proving itself as a powerful tool for phylogenetic tree construction. AVAILABILITY AND IMPLEMENTATION: MIKE is publicly available on Github at https://github.com/Argonum-Clever2/mike.git.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.